The revelation has raised concerns about why, despite repeated demands, details of the flights have not been shared with lawyers and MPs, who for years have been investigating the role played by Diego Garcia, an atoll in the Indian ocean, in the CIA’s extraordinary rendition programme.

A Whitehall official was photographed last week carrying documents marked “sensitive” confirming that the logs recording details of planes landing and taking off at the atoll have been handed to detectives. The documents, a series of printed emails and handwritten notes made by the official, reveal internal Foreign Office discussions about the line to take in response to questions about the British territory raised by lawyers and MPs.

The Foreign Office has repeatedly stressed there is no evidence Diego Garcia was used in the rendition programme, with the exception of two occasions in 2002 when two planes, each carrying a detainee, landed to refuel. But in April leaked classified CIA documents from a forthcoming US Senate intelligence committee report revealed that the US had held “high value” detainees on Diego Garcia, which has been leased by Britain to the US since 1966, with the “full co-operation” of the British government. The Metropolitan police are currently investigating allegations that an opponent of Colonel Muammar Gaddafi was rendered via Diego Garcia.

Attempts to obtain the logs, which would allow lawyers to check them against planes known to have been used for rendition, have met with stonewalling from ministers. When Andrew Tyrie, the Tory MP who is chair of the all-party parliamentary group on extraordinary rendition, demanded to see the logs in 2008, he was told “a thorough review had been conducted which had found no such information”.

The Commons intelligence and security committee has also complained in its annual reports that a lack of access to such documents compromised its ability to carry out an effective investigation into rendition, resulting in the publication of an inaccurate and misleading report. Last week, in an astonishing new twist, the Foreign Office revealed in a parliamentary answer to Tyrie that the flight logs existed, but maintained some had been lost “due to water damage”. Foreign Office minister Mark Simmonds said: “Daily occurrence logs, which record the flights landing and taking off, cover the period since 2003. Though there are some limited records from 2002, I understand they are incomplete due to water damage.”

However, blowups of the photographed emails reveal that both “monthly log showing flight details” and “daily records [obscured] month of alleged rendition” exist and are in the possession of the police.

“All relevant treaties, UN mandates and an ever-increasing body of authoritative court rulings demand that investigations into suspected state involvement in the mechanisms of torture, including rendition, be speedy, transparent and far-reaching,” said Gareth Peirce, a lawyer for several Guantánamo detainees.

“If answers to Andrew Tyrie’s direct questions have contained no mention of highly relevant logs seemingly at all times in the possession of police, then the FCO [Foreign and Commonwealth Office] has marched this country into clear violation of its most fundamental legal obligations.”

“The FCO should immediately release all documents, including the water-damaged ones, so a proper assessment can be made of this material and what it means,” said Cori Crider of human rights group Reprieve. “Only this can begin to address the decade-long whitewash of Diego Garcia‘s position in the CIA secret prison system.”